


Jigsaw

by thepurplewombat



Category: Star Trek: Alternate Original Series (Movies)
Genre: Aftermath of Torture, Bones is a BAMF, Bones pitches a fit, Jim doesn't have a clue, Khan is not okay, Khan's broken, M/M, Marcus broke Khan, Marcus is a bad man, Spock is a bit of a bastard, Stockholm!Khan, aftermath of rape, bones has some shit going on, bones is such a BAMF, everyone has secrets, jim is a bit of a bastard too, non-consensual mind-meld, torture-induced insanity/regression
Language: English
Status: Completed
Published: 2014-03-08
Updated: 2014-04-24
Packaged: 2018-01-15 00:25:37
Rating: Explicit
Warnings: No Archive Warnings Apply
Chapters: 13
Words: 17,066
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/1284364
Author URL: https://archiveofourown.org/users/thepurplewombat/pseuds/thepurplewombat
Summary: <blockquote class="userstuff">
              <p>Leonard McCoy is a compulsive fixer of things. It's what he does.<br/>So when Jim Kirk brings him a broken man, Leonard starts picking up pieces.<br/>It's what he does, after all.</p>
            </blockquote>





	1. Chapter 1

**Author's Note:**

  * For [BotanyCameos](https://archiveofourown.org/users/BotanyCameos/gifts).



“Jim, we need to talk.”

“Can it wait, Bones? It’s just, I have this prisoner I was hoping to interrogate. You know, the one who killed most of Starfleet Command?” Jim tried to keep going, but his CMO grabbed his arm to halt him.

“That’s what we need to talk about. I ran some scans on him when he came on board and Jim…this man has been through Hell. You need to be very careful with him.”

“Yes, allright, I will.”

Of course, that turned out to be harder than he’d thought, once he’d gotten to the brig and seen the prisoner sitting squeezed into the corner of his cell, eyes closed and for all intents and purposes asleep.

“Hey!” Jim shouted. “Wake up!”

Harrison jerked and his eyes flashed open almost instantly.

“My Lord Admiral?” he asked, his voice just barely above a whisper. “Has he come for me?”

“Your…” Jim paused. There was more going on here than he knew. Much, much more. “Are you John Harrison?”

Harrison nodded almost imperceptibly.

“You’re the one My Lord Admiral sent to bring me back, aren’t you,” he said, and crawled over to sit in front of the glass, looking up at Jim with guileless blue eyes. “Is he pleased with me?”

“Is he…Harrison, who is your lord admiral?”

The wrong question, clearly, as Harrison’s brow knotted and he turned his face away, eyes squeezed closed.

“Please don’t make me say his name. He has to punish me if I say it. I don’t…I know I deserve it, but I’m sorry, I…” He looked so distressed that Jim rushed to reassure him.

“That’s fine, Harrison, you don’t have to say it. Um…would you like something to eat? I can have something brought for you, if you want.”

But Harrison shook his head.

“My Lord Admiral will feed me,” he said simply. If his ‘Lord Admiral’, and Jim was having some sickening suspicions as to who that might be, had been feeding him, he’d been doing a shit job of it. Harrison was lean almost to the point of being emaciated, nothing but muscle over bone. “When will he come for me?”

“I’m sorry, Harrison, but I don’t know. I’ll have more questions later.”

The man just nodded and kept watching as Jim left. Jim tried not to run.

“I _told_ you,” Bones said sternly. “I fucking told you, and you didn’t listen. Look at this,” he said, and pulled Harrison’s file up on one of the big wall display. “See this? These here are the signs of forced emesis. It wouldn’t have left scarring like that from just one session, someone or something made him throw up repeatedly over a long period of time. You wondered why his voice is like that? This is why. _This_ is a beating. No more than two weeks ago, and if he didn’t heal like nothing I’ve ever seen before he would be dead right now. These scars right here are _surgical lasers_ , Jim. Do you see that line over there? Someone took off his arm and reattached it. I can’t tell how long in between procedures, but there’s no way that was accidental. Nothing in the galaxy can take off a limb that smoothly by accident. This man was tortured for months. Probably years, from the aging of some of the scars. Speaking of which, look at this. It’s on the back of his hand.”

 _My name is John Harrison_ , it read, in scars that had faded to white with age.

“Christ,” Jim said. “That looks painful.”

“It would have been. My scans say it was etched with acid. It would have been excruciating. I’m going to have to insist that I go in with you the next time you want to talk to him, Jim.”

Jim nodded.

“Of course, Bones. You need to…let’s go.”

Harrison was just where Jim had left him, sitting cross-legged in front of the glass, watching the comings and goings in the brig with interest.

Bones settled himself on the ground in front of him.

“Hi,” Bones said. “I’m Doctor McCoy, but most people call me Bones. What’s your name?”

“John. John Harrison,” the prisoner offered. He didn’t glance at his hand, but he did touch the scarred back of it lightly.

“Is that the name your mother gave you?” Bones asked.

Harrison shrugged.

“Freaks don’t have mothers,” he said. “My Lord Admiral says my mother was a test tube. He’s right, of course.”

“Did your admiral give you the name Harrison?” Bones asked. Jim had never seen him speak that softly, be that gentle, before. Harrison seemed to be puzzled by it, more than he had been by Jim’s harsher questions.

“I…yes?”

“So you had a name before Harrison. What was that?”

“I’m not allowed to say it. It’s not my name. I’m not supposed to remember it.”

“But you do?”

“It’s not my name,” the prisoner said almost desperately. “My name is John Harrison, I _promise_ it is. That other name isn’t mine, not anymore, it never was.”

“John!” Bones snapped, and the prisoner’s eyes opened and fixed on him. He was on the edge of hyperventilating now, and pale as a ghost. “Supposing that we were to stipulate that your name is John Harrison. That’s always been your name, yes? And supposing that we stipulate that that _other_ name had nothing whatsoever to do with you. It’s just some words in your mind, yeah?” The prisoner nodded. “Then, keeping those stipulations in mind, do you think you could tell me what that name is?”

“I could…I could try…” the prisoner offered.

“Okay, go ahead and tell me the name.”

There was a long pause. Jim almost thought that he wasn’t going to answer.

Eventually, though, he did.

“Khan,” he blurted, eyes closed and practically cringing. “Khan Noonien Singh. But it’s not my name now, my name is-“

“Yes, I know. Thank you for telling me this. Are you hungry?”

“My Lord Admiral will feed me,” the prisoner – _Khan_ – said, but Jim didn’t miss the convulsive movement of his throat.

“Your Lord Admiral may be awhile. Maybe you should eat something while you’re waiting for him?”

“Don’t try to trick me,” Khan said flatly. “I know the rules now, I’m _good_ now, and my Lord Admiral will feed me.”

“Of course,” Bones said. “I’m sorry, I forgot. Are you allowed to drink?”

Khan nodded cautiously.

“Water. May I have some water, please?”

“Of course,” Bones said, getting to his feet. Khan looked up at him from the floor, and he looked absurdly childlike in that moment, open-faced and almost innocent. “I’ll send someone down with some soon. You should get some rest.”

Jim followed his doctor out into the hall beyond. Bones was muttering to himself. Most of it seemed to be obscenity of some kind.

“Bones?”

“Do you know,” Bones said, “that the man we have in our brig right now, the man who had a panic attack at the thought of telling me his _name_ , used to rule most of Earth?”

He thrust his datapad at Jim, who stared down at the long-haired, tanned man in the picture. It was their prisoner, if you took away the long hair and the expression of command and added a Starfleet uniform.

“Someone found him, somehow, and they tortured him until he _broke_. How much pain do you think it would take to break an augment, Jim? What would you have to do to him, to make him scared to say his own name? I need some time to think about a treatment plan for him. You, Nurse. Take a litre of water and fortify it with every vitamin and mineral you can get your hands on. I’m not having a prisoner starve to death in my brig.”

“He’s a criminal, you know,” Jim said when the nurse had gone. “He killed a lot of people.”

“You saw him, Jim. That man is _broken_. He wouldn’t have done that without permission from his _Lord Admiral_. Not in a million years.”

“Then I guess,” Jim said, “We need to find out who that is, don’t we?”

**Notes for the Chapter:**

> Someday I will be able to scroll past a post by Botanycameos and not immediately have sixteen different fic ideas for this damn fandom.  
> Today...is not that day.
> 
> Also, don't expect this to be the only version of Stockholm!Khan I do. BC had so many excellent suggestions I just couldn't pick one.
> 
> Botanycameos is basically my Star Trek fic muse.


	2. Chapter 2

**Notes for the Chapter:**

> I don't have a beta, so if you spot a typo please come and yell at me about it in the comments. I'll probably be mortified, but I promise I'll be more mortified if I spot it on a reread three weeks from now.

 

Bones woke at 3am to the sound of an alarm. There were always alarms going off on the Enterprise, either because Jim had done something stupid with the ship, or because Spock had done something stupid with the computers. He’d basically started blocking them out, which was why he’d taken the precaution of programming his own set of alarms into his communicator.

This one was keyed to the poor bastard in the brig, and it said that he was dying.

Leonard McCoy believed in very few things. God had proved to be a disappointment, true love was a pipe dream and Starfleet was as corrupt and slimy as any other big organization. But the one thing he did believe in was that doctors had superpowers.

Specifically, the power of teleportation. It was the only way to explain how he came to be storming into the brig, fully dressed and already shouting at the incompetents manning the station three minutes after waking with no memory of actually putting any clothes on.

He checked just to make sure, but he actually was dressed. Clearly, God loves doctors.

He was through the forcefield the moment it cleared, and on his knees beside his patient a second later.

“Bloody buggering Jesus,” he swore as he ran a scanner over him. “Oh, admiral whoever you are, you are going _straight to hell_.” Then he stabbed at his communicator and screamed at the idiots in the transporter bay until they beamed the both of them to sickbay.

“Nurse, I need…what do I need…I need antidotes!”

“Which ones?” Chapel asked, coming to his side to help him lift Khan/Harrison onto one of the sickbay beds.

“Fucking _all of them_. Look at these readings, he’s got an implant pumping every damn toxin I can detect into his system. Now, _go!_ ”

Chapel was many things, and she had fucking awful taste in men, but she wasn’t stupid, and instead of following his rather frantic and stupid order (which he later realised would have killed his patient as he injected dose after dose of antidote into his system), she held up a blood filter instead.

“Oh, _yes_ , Chapel, you’re fucking gorgeous, hook him up and then hand me- no, you focus on that, I’ll get my own damn scalpels.” Because the blood filters she was hooking up to every artery she could get her hands on would clean the poison out, but that wouldn’t do a damn lick of actual good if he didn’t get the implant out.

Three hours later, Bones tossed a jagged, be-tendrilled piece of metal into a kidney bowl and sealed the last of his incisions. Khan/Harrison was still unconscious, with filters like leeches stuck everydamnwhere and an angry red slice across his abdomen. He was fucking _skeletal_ , whipcord muscles and not an ounce of flesh. He didn’t have as many scars as Bones had expected. There was one, a perfect band around his upper right arm. Thin lines, barely proper scars at all, crisscrossing his torso. The bottoms of his feet were a mass of scar tissue. Someone had taken off all the skin there and…he couldn’t think too long about what that must have been like. Careful manipulation proved that the scar tissue restricted his feet, so Bones stuck a regenerator on it, to soften and remove and repair. When he was done, his patient was looking at him.

“You’re in Sickbay,” he said. Wouldn’t make the poor bastard ask; that had probably not gone well for him in the past. “You had an implant, it was killing you.”

“Oh. Was I…did I do something wrong? Did I…” He trailed off, clearly confused.

“I think it was to stop you escaping. It was set to dispense poisons into your blood if a certain code wasn’t typed in for a period of time. Did you try to escape a lot?”

“At first,” Khan admitted reluctantly. “My Lord Admiral had to punish me many times, in the beginning, until I learned how to behave. He even had to damage my feet because I didn’t know any better than to run away.”

Bones helped him sit up, watching him carefully. Khan’s hands didn’t go to his crotch; he didn’t try to cover himself at all. Nothing left to build on there, then. Some of his readings were starting to make more sense now, too.

“Khan-“

“John! My name is John Harrison!”

The poor bastard’s expression was so terrified as he looked around that Bones took two steps back, hands in the air.

“Okay, okay. John. Did your admiral ever…” _Christ, I did not sign up for this shit_. “Did he touch you, John?”

“Of course,” the man said readily. “He didn’t like to touch me but he had to, to make me better. He can’t teach me the error of my ways without touching my filthy freak skin. Sometimes he tried, though. When I was particularly bad he would send me to the barracks. I didn’t…I don’t like the barracks much. They like to make me bleed.”

_“_ Jesus _wept_ ,” and what the bloody buggering fuck was he supposed to do with that? Where did he even _begin_ to fix this?

The augment slithered to his knees in front of Bones, looking up at him with a pleading expression. The expression sat all wrong on that chiselled face, and that body had no _business_ knowing how to kneel.

“Please,” he said softly. “Don’t tell My Lord Admiral what I said about the barracks. I did deserve it, I really did. And he said because my body responded I must have enjoyed it, so…please don’t tell him? I can…I can be good for you…”

Khan’s shaking hands came up to pluck at the front of Bones’ trousers just as if his meaning wasn’t clear. Bones closed his eyes for a moment and breathed through his nose, and tried not to think of what you would need to do to turn Khan Noonien Singh into _this_ , kneeling at his feet and begging McCoy not to tattle on him.

Of course, he already _knew_ what had been done. That made it so, so much worse, because suddenly it wasn’t Khan at his feet, it was any of a dozen men and women who’d passed under his hands once upon a time.

Once upon a time he would have smiled and run his hands through Harrison’s hair and allowed him to buy his silence. Once upon a time.

But not now.

Now, Bones took both Khan’s hands in his and pulled him to his feet. The man towered over him.

“I don’t want that from you, John. Not now. But I’ll make you another deal.” Bones spun away and fetched something from the cooler. “This is a protein shake. Technically, it’s a liquid, so you can drink it. But your admiral would probably object, because it’s nourishing, and he doesn’t want you to have nourishment from anyone else. Sounds right?”

Khan nodded.

“Sometimes I would get hungry, and the men would give me food. I would throw it up and be sick. I learned better. Only My Lord Admiral can feed me. He knows what I need.”

“Right. Well, he’s not here, and the implant is gone. I’m betting that if you drink this, you won’t get sick.”

Khan shook his head.

“It’s not _allowed_ , Doctor. I’m not…” but his eyes followed the tall glass in Bones’ hand, and his hands shook and curled into fists. “I’m not allowed.”

“It’s liquid,” Bones said. “You can drink it. It will keep you alive until your admiral comes, and he won’t have to know. Not about the shakes, and not how you feel about the barracks. Sound like a deal?”

It’d sound like what he was used to, to Khan, a Kobayashi Maru of a deal that’d leave his life in Bones’ hands either way. But he clearly believed that his admiral would be more upset about the barracks than the food, assuming Bones would even keep any part of the deal – or he was so hungry that he didn’t care anymore – because he snatched the glass and put it to his mouth, gulping greedily at the nutrient shake.

Bones couldn’t stop himself. It was just a moment’s weakness, he told himself. He wasn’t slipping into old habits. Khan had needed the reassurance.

That was the only reason that he petted the augment’s hair and murmured “there’s a good boy. Drink it all up. Good _boy_.”

The only reason.

**Notes for the Chapter:**

> Um, so...apparently there's more to the good doctor than I thought.
> 
> I officially have no fucking clue what's going on anymore.


	3. Chapter 3

After getting two nutrient shakes into him, Bones dug into the patient cupboards until he found a pair of sweats, worn soft and thin by repeated washings, and helped the man into it. The top was too big for him and slipped down one shoulder, exposing the jagged peaks of his collarbone, but it didn’t strain over the filters still clamped on his arms and legs, and that was the important thing.

“Do you think you could sleep?” he asked, when he had his patient dressed. “You need a bit of rest, I think.”

Khan nodded gratefully and Bones helped him onto the cot he used himself, when he needed to sleep in Sickbay. It was more comfortable than the patient beds, and with as skinny as Khan was he would need the extra padding.

“You okay with the light being on?” he asked, and he didn’t miss the look of gratitude Khan sent him. “Right, I’ll leave them on then. I’ll be over here, doing some paperwork.”

He sat down at his desk, listening to Khan’s quiet breathing as he called up file after file.  He was elbow-deep in studies of PTSD and Stockholm – all concepts he was familiar with, but from a completely different point of view than he needed now – when Jim came storming in.

“You took the prisoner out of the brig? What the actual _fuck_ , Bones? You can’t just do that, what if he’d gone berserk?”

Bones held a hand up to silence his overly loud captain, and ushered him out.

“He’s sleeping. And before that, he was being poisoned by this little number.” Bones held up the implant, careful of the spikes and razor tendrils. It had been designed to burrow itself in, to attach to the nervous system of its host and grow and grow. Somewhere out there, there was a control pad for it, a simple palm-sized device that would have once controlled every facet of Khan’s biology. “It’s a control chip, and I’d rather you didn’t ask me how I know about it. It tied itself into his nervous system and worked by remote control. With the control in hand, you could control…everything. Pain or pleasure at the touch of a button, Jim. It made him throw up if someone other than his controller fed him. It probably made him respond to them in every way. Terribly useful little thing,” Bones said absently, stroking one of the little device’s vicious curves. “There’s no simpler way to break someone’s mind than to turn their body against them.”

Jim was staring at the implant with an expression of horror on his face.

“So…someone was _remote controlling_ him back on Earth? Like some kind of…puppet?”

“No. Weeel, not quite. This model isn’t complex enough to actually substitute for a brain. Not without at least several years’ more grow time. It couldn’t have moved his body for him. But that man in there…from the age of some of the scars on him and from the growth on this little monster he’s been in captivity for more than a year. That’s a year during which he couldn’t rely on even his own body to tell him what’s real or not. You have someone that long, they’ll do anything to please you. Kill, die…it doesn’t matter. They’ll do _anything_.”

Jim was looking at him now with a speculative expression.

“How do you know so much about…”he waved a hand to indicate their entire situation…”all this?”

“I’d really rather not talk about it,” Bones said, and turned away. It was bad enough that Khan was here, in his sickbay and so damn beautiful. A shattered image of a man just begging for Bones to put him back together. It brought back memories he’d thought safely buried, longings he’d taught himself to ignore.

“Bones…”

“Dammit, Jim, I said I don’t want to talk about it!” he shouted. Through the window, he watched his charge curled up on his bed, twitching occasionally with nightmares. What kind of dreams did Khan have now? Would Khan tell him, if he asked?

“Okay. Okay, I won’t…He needs to go back to the brig, though. He’s still a prisoner, Bones, and we don’t know what else he might have been programmed to do.”

“No, I need him here,” Bones’ mouth said without his permission, and he clenched his hands in front of him. “He’s a patient at the moment, not a prisoner. Set guards on the doors to Sickbay if you want, but they’re really not necessary. I need space to work on him, time to undo the damage that’s been done.”

“You have a week,” Jim said after a while. “A week, then we’re back at Earth. Do what you can, but when we get back to Earth we’re going to have to decide what to tell the Admiralty, Bones.”

Bones nodded and his captain left.

Bones stood for a long time staring through the window, watching Khan’s restless sleep.

 _Oh, Leonard_ , he thought sadly, and his mental voice sounded like his grandmother. _What have you gotten yourself into now?_

**Notes for the Chapter:**

> So our power came back on, finally!
> 
> There's still a bit of flooding around, but all is well at casa Mortis, and as an added bonus, my brother is moving in with us today! Which means, more effort needed to hide the porn. There's a downside to everything.


	4. Chapter 4

**Notes for the Chapter:**

> Some Khan POV. Let me know what you think of him. Is he awful? Should I get out of his head and never attempt to write Khan again? Inquiring minds want to know!
> 
> Also, you may notice that my description of Bones does not exactly read like Karl Urban. This would be because the McCoy in my head will always be DeForest Kelley. Everyone else, feel free to imagine their AOS counterparts, but if my description of Bones doesn't make sense, just remember that in my head, he's a skinny angry wrinkled Southern man with bad hair and electric blue eyes who likes romulan ale and insulting people, not a pouty beefcake with fabulous hair.
> 
> Not that I have anything against pouty beefcakes with fabulous hair, you understand. I'm greatly in favour of the species in general, and Karl Urban in particular. His hair really is fabulous.
> 
> And now...to the story!

John woke slowly. He couldn’t remember the last time he had been allowed to sleep as much as he wanted, or as little. It had varied, under his lord Admiral’s care – some days he was made to sleep much longer than his body wanted, and other times he went weeks without. Either way, he stayed slow and stupid and erratic, no matter how much care his Lord Admiral took to try and fix him.

The doctor was sitting at his desk not far from the cot, deep in thought, but he looked over as soon as John moved.

“Feel better?” he asked.

“Yes,” John said, after a moment to think about which response was the least likely to get him punished. “Thank you,” he added after a moment.

The doctor smiled, his bright blue eyes almost lost in a nest of deep wrinkles.

“Good, good. Can you take those off for me and hop onto that examination table, please?”

John obeyed with alacrity, leaving the garments folded neatly on the bed and waiting patiently for the doctor to attend to him.  He studied him while he waited. Doctor Leonard ‘Bones’ McCoy, his file had read. Chief Medical Officer of the USS _Enterprise_. Formerly of Section 31. His research had been amazing, at least if the samples John had been allowed access to for his work was any sign. His pathogens were elegant and vicious. John had been particularly fascinated by Pathogen FH-X541 – the Klingon plague. It had been beautiful, almost lovely enough to forget its purpose.

Suddenly the doctor was in front of him, and John blinked in surprise. Was McCoy that quick, or had he been woolgathering?

“I think we can take these off now,” the doctor said, taking hold of one of the leech-like purifiers attached to John’s limbs. His other hand was shockingly warm on John’s bare shoulder, his rough fingertips like brands against John’s skin. His enhanced senses were a mixed blessing. On the one hand, it allowed him to feel things like McCoy’s gentle hand on his skin with crystal clarity. On the other, it also enhanced the disgusting sucking feeling of the purifier extracting its dendrites from his skin. John shuddered helplessly and closed his eyes, dropping his head against McCoy’s shoulder. If he was punished for his forwardness, so be it, but he didn’t think that McCoy would punish him for this.

He was right. The doctor said nothing, just shifted his hand to the back of John’s neck and stroked soothingly.

“You ready for the next one?” he asked after a moment. John nodded against him and closed his eyes, trying to filter his perceptions. He’d been able to do that once, he thought, in the time before. It was so much harder to gather the necessary focus now, to keep his mind on the gentle fingers in his hair and ignore the slow retreat of the purifier on his thigh.

Finally, that one was done, too, and John relaxed with a sigh. Only two left now. Only two to go, and McCoy was switching hands so he could touch the one on his other arm.

“Only two more,” McCoy murmured as it started.

John grabbed hold of the doctor’s coat with his free hand and gasped quietly, because this one _burned_. He couldn’t stop the tiny whimper that escaped him as the feeling of fire in his veins spread all down his right arm, making his fingers twitch against his will.

“Shh, shh,” the doctor said. “There was a great deal of damage to that arm. The purifier had to clean out your veins as it went, it’s going to hurt quite a bit. It’s sending a disinfectant through that part of your system now.”

 _Quite a bit_ was an understatement. He was on fire, he was burning up from the inside out, and he bit his lip on the moan that wanted to escape.

Was this a punishment? Had he done something wrong and not realised?

“I’m sorry,” he sobbed, on the off chance that an apology would make the pain stop. Sometimes, in the past, that had worked. “I’m sorry, I won’t do it again.”

McCoy pulled his face away, his blue eyes looking at John with concern.

“This is not a punishment, John. This is a medical procedure, do you understand? I’m sorry that it hurts, I really am, but if you want to regain the full use of that arm this has to happen.”

John nodded and closed his eyes, and the doctor guided his head back down to rest on his shoulder.

“Not much longer now,” he said, and John almost wept with gratitude. He turned his head and drew in the comforting woodsy-minty smell of McCoy’s skin, using it as a distraction. He pressed a kiss under the doctor’s jaw, just above the collar of his uniform shirt, and noted that McCoy went absolutely still against him. There was no punishment forthcoming, so he did it again, a light and cautious sucking kiss, his tongue flicking out against salty skin.

His free left arm went around the doctor’s waist entirely without his permission, pulling the other man against him, and he hummed in contentment as he felt McCoy hard against his stomach. This was good, this was easy, this was what John Harrison was _for_. And McCoy had been so good to him, so _kind_ , he wanted…he’d just been trying to distract himself from the pain, but now the pain was gone and McCoy smelled delicious and tasted even better, and John wanted to go to his knees for him so very much, wanted to make McCoy happy because then perhaps McCoy would keep him and keep being kind to him.

He hadn’t realised that he was moaning softly until McCoy’s hand clenched abruptly in his hair and pulled him away. John didn’t resist, but pulled away and let the doctor go. 

“I’m sorry,” he said immediately, putting his hands on his thighs to stop their shaking. Both of them were clear of machines now - McCoy must have done the last one while John was distracted. “I thought you wanted…”

“John, you don’t have to do that for me,” McCoy said, his tone gentle even though his voice was wrecked, even though John could see the outline of his erection through his uniform. “You don’t have to…offer yourself to me like that.”

What if…” John took a deep breath, steeling himself, and then he took a risk. “What if I wanted to?”

McCoy raised a single eyebrow at him.

“You don’t know what you want, my friend.”

And something in his wry, amused tone made John think that perhaps it would be okay if he…disagreed. Just a little.

“I…” but he couldn’t find the words to explain that McCoy’s was the first kind touch he’d felt since he woke up so many months ago, that he smelled and tasted like safety and home and good things, that John wanted him to touch him because he thought maybe it would be nice, even though he didn’t deserve it and even though his Lord Admiral would have to punish John for it later, to have someone touch him who, however misguided they were, thought that John was a person. “I want...”

Words failed him and he reached out instead, sliding a hand up McCoy’s chest and along the side of his neck until his fingertips rested against the place he’d been kissing.

“I want,” John said again, and watched as McCoy’s hand came up to cover his and pull it away gently.

“And if you still do when you can hear the name Khan Noonien Singh without cringing, you can have. Is that a deal?”

John hadn’t been able to stop himself from flinching at the sound of that name, but he nodded.

“Can I…”

McCoy waited, but John’s courage had left him again and he just gaped stupidly. God, what was he thinking? He really was pathetic, wasn’t he. His Lord Admiral was right to be disgusted with him.

“You can ask anything, John. I won’t punish you.”

“Can I hug you?” the words popped out without intervention from his brain, and he hastened to clarify because McCoy looked absolutely _stunned_. “Not right now. Well, yes, also right now. But sometimes, when I was scared, my lord admiral used to let me hold him and it…it helped. Can I…” McCoy nodded, and John slipped off the table to kneel at his feet. He was about to reach out cautiously to touch his leg when McCoy dropped to his knees in front of him.

“What are you doing?” he asked, and if his voice was pleasant his eyes were icy.

John’s words left him again and all he could do was wave a hand helplessly. For a moment, it looked as though McCoy was about to cry.

“Was that how your lord admiral let you hug him?” he asked, and John nodded. McCoy muttered something  under his breath that sounded obscene. “That’s not how I hug. Let me show you how you hug me,” he said, and reached out and gathered John in his long arms, pressing him against his chest almost like he’d been holding him before. “Now you put your arms around me,” he said pleasantly.

John reached out cautiously, wrapping his arms around McCoy’s torso as gently as he could manage; the last thing he wanted to do was hurt McCoy with his freakish strength. McCoy let out a sigh and rested his chin on the top of John’s head.

“That okay, then?” he asked eventually, and his voice vibrated against John’s ear where it was pressed against his chest.

John nodded. It was warm in McCoy's arms, and McCoy's hand was back in his hair, stroking his scalp with long soothing motions, as though John were a cat or a tribble.

“That’s good,” McCoy said. “Feel better yet?”

John nodded again, closing his eyes to better catalogue the warmth against his skin, the sound of McCoy’s heart in his ears. His entire body was limp with comfort.

“Good,” McCoy said. “That’s good. Now, help an old man up off the floor, would you?”

**Notes for the Chapter:**

> And now we know what Bones' deep dark secret is.  
> ooooeeeeeoooooooo
> 
> Also, it looks like the pairing is going to be Bones/Khan in the end. I hope nobody is too disappointed.


	5. Chapter 5

Bones had been right. Khan was exquisite on his knees, his mouth stretched around his cock, tears leaking from his eyes. Someone had put a lot of time and effort into training him in this, and he lavished every hard-earned bit of skill on Bones’ cock, pulling off every now and then to mouth at his balls, or to swirl his tongue around the head as though it was the world’s tastiest lollipop.

He didn’t protest when Bones put his hands on the back of his head and slid himself slowly deeper, until Khan’s mouth was sealed around the base of his cock, and the head had gone down his throat. Of course he didn’t protest, he’d never protest. He just swallowed convulsively and then relaxed, eyes still closed, and let Bones take his pleasure, fucking deep and hard into his throat, continuing the rather lovely work his previous owners had been doing on the augment’s voice.

He came with a groan, balls-deep in Khan’s face, and woke up sticky.

Bones sat up and glared at his lap.

“Oh, for fuck’s _sakes_ ,” he muttered. It was 5AM, and he’d been asleep for all of three hours, after returning Khan to the brig – temporarily, but he wasn’t as young as he used to be (the state of his sheets aside) and a man needed his beauty sleep. He might as well get up, then, and go see about his patient.

Khan was sitting in front of the glass again, watching the world go by, and his face lit up when Bones came in. That…didn’t bother him as much as it should. He didn’t want to be the augment’s new _Lord Admiral_. He just wanted to fix him, to undo the damage his captors had done. And if he had a few dreams that said otherwise, and a little voice in the back of his head that called him _dear doctor_ and begged so prettily, that was no concern of anyone’s.

“Morning, John,” Bones said. “Feel like coming to Sickbay with me today?”

“Of course,” the augment said and slithered to his feet. He looked softer now, in the too-big sweats he’d kept because his black Starfleet uniform was ruined, his slender feet bare against the cool floor. He looked like a child, almost, with his hair out of its carefully controlled style and falling into his face, and the fragile elegance of his collarbone exposed by the too-big neck of the shirt.

The red-shirted security guard scowled at Bones, but he’d spent the better part of his twenties and thirties staring down men twice as big as him (but only half as mean, and none with his reputation), and the man backed down and opened the cell. Khan stepped through immediately and stood in front of Bones in a sort of parade rest that somehow, magically, made the augment look shorter than him.

That was another clue, then. Whoever Khan’s ‘Lord Admiral’ was, he was shorter than Khan. That pose had to have been practiced.

“Come on, then” Bones said, and left, trusting that Khan would follow (he did) and that security would sort themselves out (they did). The ship’s corridors were just coming alive when they left the brig, and Bones could sense Khan becoming more and more tense behind him. His breathing became faster and shallower, until Bones had to reach back and take hold of his wrist, and remind him to breathe.

He didn’t blame the man, obviously. He’d been in a similar position, once, and had much the same kind of looks levelled at him (and what did they know, anyway, of what a young man was willing to do, to pay, to become a doctor, and _who were they to judge him_?), and had had…a much worse reaction.

Soon, although not soon enough by half, they were alone in Sickbay with the doors thankfully closed, and Bones didn’t need Khan’s pleading look to know what the man needed. He opened his arms and the augment fell into them as though his strings had been cut, wrapping his arms around Bones and burying his head in his chest.

“I shouldn’t care what they think,” Khan said, after a long silent moment. “Before I came here, that’s how everyone looked at me. Like I was…dirty. It didn’t matter then, why does it matter now?”

“Because you’re not there anymore, and some part of you is starting to realise that, and because you’ve spent two days talking to only me, and I don’t look at you like that,” Bones said. “It’s one thing when everyone looks at you like the dirt under their shoes. It’s different when there’s someone who doesn’t.”

Khan took a deep breath and stepped back.

“Thank you,” he said. “How do you…you know a lot. About…about how it feels to be me. And about…how I feel about My Lord Admiral.”

Bones sat down and waved Khan into the chair opposite.

“You’re curious,” he said, and Khan closed his eyes the way he did when he was steeling himself, and nodded. “It’s simple enough. I’ve been where you’ve been. Both sides of the equation. I…graduated, you might say.”

Bones picked up a stylus from his desk and kept his eyes on it, fiddling with it as he told Khan the story of a young man of great potential, who wanted to become a doctor very badly, who’d gotten himself indebted to the worst parts of Starfleet to do it. How he’d survived a brutal apprenticeship and become a monster to do it.

“You’ve seen some of my work, I think,” he said, and Khan nodded.

“FH-X541,” Khan said. “I modified it to use as part of the payload of the special long-range torpedoes My Lord Admiral had me build. It was beautiful. Modifying it felt like sacrilege. It was...inspired.”

“Hmm. I was actually pretty proud of that one. Got the idea from a 20th century computer game. Lower Klingon fertility to 10% of normal, let their violent natures take care of the rest. My models predicted extinction within 150 years.” Bones carefully didn’t let his expression change as he made note of the two very important facts he’d just learned.

“Mine said 50,” Khan said. “But then, they were based on using the long-range torpedoes as a delivery system, which had an 89% chance of starting a war. Even if they won, they wouldn’t survive.”

Bones sat back, staring at Khan.

“That’s…impressively twisted.”

Khan flushed with pleasure and looked away, and Bones took up the thread of his story. He glossed over the fifteen years he’d spent in the depths of that hell, skipped over most of his experiments entirely. He spent a lot of time on what had happened to him after his unit was shut down, when he was retrieved; the trials (thank God his file had clearly showed his age when they’d recruited him or he would have spent the rest of his life in a penal colony), the endless months of therapy…

“It becomes easier, with time,” Bones said. “Sometimes whole days go by when I don’t think about that time at all.”

“But I _miss_ him,” Khan said miserably, his eyes fixed on his hands where they coiled restlessly in his lap. “Even though he hurt me, even though you’ve _explained_ , and I’ve done the reading, and I understand exactly how he did what he did to me, I still miss him. Will that go away too?”

Bones sighed.

“I’m sorry, but probably not. If my old master were to walk in here today, I’d be on my knees before you could say ‘boo.’” He said nothing about the dreams, where he woke up shaking and sweating, terrified and hard as a rock, and had to turn on every light in his quarters before he could breathe again, before he could be sure that he was as safe as possible. He had a feeling he'd be having one of those tonight. Pity. He wouldn't have minded another Khan dream.

“I’m going to leave you alone in here for a minute,” Bones said, and got to his feet. “There’s some files on this datapad I want you to look at. They’re what I’ve been able to reconstruct of your medical records. If there’s anything missing or incorrect, make a note of it.”

Three long strides and he was out the door, nodding to the security guard as he passed, keying his comm to page Kirk and Spock to the conference room.

 _Of course_ , he thought bitterly. _Of course his ‘Lord Admiral’ was going to be Alexander Marcus. Who else would it possibly be? Why didn’t you put the pieces together sooner, you absolute_ moron _?_

Of course, when he’d given Bones his names, he’d been ‘My Lord Commander,’ but that was hardly unique in S31. Bones should have  _thought_ , should have  _realized_. He'd been unforgivably stupid, and now they were two days out of Earth and their ship was packed to the gills with what could be called weapons of mass destruction, if you were feeling in an understatemently mood.

“Jim, Spock,” he said, storming into the conference room. “I know who had Khan, and I know what his plan.”

**Notes for the Chapter:**

> So...yeah.
> 
> You guys, I officially have no fucking clue what's going on here.


	6. Chapter 6

**Notes for the Chapter:**

> This chapter contains description of an unwilling mind-meld.
> 
> Also, I don't think it should surprise anyone at this point that the theme song for this fic is Jace Everett's 'Bad Things.'

“I don’t believe it,” Jim said immediately. “Admiral _Marcus_? He’d never…Bones, how can you be sure Khan isn’t playing you?”

There were so many possible replies to that, most of which involved profanity. The others all revealed things Bones would really rather not tell his only two friends.

He settled for glaring at Jim, who at least had the grace to look embarrassed.

“Sorry, but…how _can_ you be sure?”

 _Because the only time a human being tells the truth is when they’re broken, and because Khan is about as broken as they come, and I should know_. That was one of the things Bones didn’t say. He wasn’t sure what he was planning to say, but Spock jumped in before he could.

“There is, of course, a way to find out what Khan knows without a doubt. I was hesitant to suggest it before, but…”

“You want to mind-meld with him?” Bones asked, and if he couldn’t keep the horror out of his tone, well, nobody could blame him. “Spock, have you got any _idea_ what you’re suggesting?”

The damn green-blooded hobgoblin looked profoundly unconcerned.

“It is the logical alternative, Doctor.”

“No, it’s _not_!” Bones roared. “It’s sick, and I won’t stand for it. That man is in _my_ care, and I will not let you _violate_ him like this, do you hear me? Jim, I’ve told you what I found out, which is what you wanted me to do. Alexander Marcus was Khan’s owner, and he was planning to use the Enterprise to provoke a war and eliminate the Klingons once and for all. Now, if you’ll excuse me, I have a patient to attend to.”

And he stomped out.

Khan was just where he’d left him, making careful notes on his medical history.

“I hadn’t known how much damage they did,” he said as soon as Bones stepped into Sickbay. “If I hadn’t been an augment, I doubt I would have survived.”

“Oh, you would have,” Bones said. “You wouldn’t have _liked_ it, but you’d have lived. They were very careful, you know. Not as careful as they’d have needed to be with someone who didn’t have your gifts, but careful enough. Come here, it’s time for your shake.”

They’d tried to start Khan on solids, the day before. It had been a disaster – even without the implant Khan couldn’t keep down solid food. He’d had a panic attack and puked all over himself and Bones, and it had taken McCoy hours to calm him down and assure him that he wasn’t going to be punished.

Khan swallowed the shake without protest, even managing a smile for Bones. He was making incredibly rapid progress, considering what he’d been through, and- Bones’ thoughts were cut off with the buzz of an alarm.

“Damn it,” he muttered. “There’s been an accident in Engineering. Hand me that kit, please, I’ll be back in just a few.”

 

Medical kit in hand, he stormed off, leaving John alone in the Sickbay. He went back to looking over his records. Many of the injuries in the file, he didn’t even remember. He’d been so out of it for a lot of the time he’d spent in his Lord Admiral’s care (he still couldn’t even think his name without wincing) and there had been so _much_ pain…

He looked up as the door slid open, thinking it was McCoy again, but no. It was the captain, and at his side a Vulcan with a stern expression.

“Doctor McCoy isn’t here,” John said, wanting to be helpful. “He said something about an accident in Engineering.”

“We know,” the captain said. “We’ve come to talk to you. Doctor McCoy has told us some things that he found out from you. We need to confirm them.” He gestured to the Vulcan as though that should be self-explanatory, which of course it was.

John’s hands began to shake and he hid them in his lap, but there was nothing he could do about the fact that he knew he’d gone absolutely bone-white. The Vulcan took a step closer to him, and he stood up out of the chair and took a step back.

“I’d…really rather not,” he said, and hid his shaking hands behind his back.

“I’m sorry,” the captain said. “Spock, go ahead.”

The Vulcan reached for him and John ducked under his hand and dodged away, because he was _allowed to say no_ , McCoy had said so.

He headed for the door without any clear idea of what he’d do once he reached it, but the captain had come prepared. The tangle field caught him in the back of his knees and he went down like a sack of grain, knocking his head hard against the floor. The Vulcan – Spock – knelt next to him and turned him over, his unchanging face still blank.

“Please,” John whispered, with no hope that he would be heard, and tried to stop the tears from spilling over. “Please, don’t.”

“Just relax,” the Vulcan said, and began the merge.

He was in John’s mind the next moment, rifling through his memories. At least he was efficient, not like the ones before, who had…he paused in his examination of John’s childhood.

 _You’ve been melded with before_ , he said. Of course John had been melded with before, Spock was just being stupid now, and then the memories of his time at Section 31 started flashing before his mind’s eye _no no no_ , he didn’t want Spock to see that, didn’t want _anyone_ to see him like that, naked and bloody and begging, and he didn’t…

Spock moved on to the time after he’d been brought aboard the _Enterprise_ , reviewing his interactions with McCoy, and John’s horror grew, because he couldn’t, some secrets weren’t _his_ , and he wrenched his mind out of Spock’s control and deliberately thought back to Section 31. He threw the images at Spock as though they were weapons, no longer caring for the last tattered shreds of his dignity, because McCoy had trusted John with his secrets and he was going to _protect them_ no matter the cost. After an eternity it wasn’t so bad anymore. He hurled memory after memory at Spock, who watched in horror as Khan was taken again and again, and broken and made to kneel. He recoiled in revulsion as Khan was raped by a Vulcan with dark red hair and a mask, who invaded his mind with the most exquisitely detailed hallucinations. Eventually Khan was gone and it was just John, kneeling at his Lord Admiral’s feet, sucking him off desperately because if he was good enough he could save…

The bond broke with an audible _crack_ , and John blinked up at the ceiling, dazed. Then he realised that McCoy was standing over him like an avenging angel, and Spock was reeling backwards, blood pouring from his nose.

“Release him,” McCoy said – _snarled_ , really. The tangle field vanished and John knelt, resting a hand on the back of McCoy’s calf. He was still shaking and he really, _really_ needed the comfort of McCoy’s arms and the smell of him, but he couldn’t have them because the captain and Spock were _right there_. Bones was shouting at them both, almost incoherent in his rage, and they were both just staring at him in a dazed sort of awe. After a minute, during which he was ignored, John crept closer and rested his head on the back of McCoy’s leg too. McCoy turned to look down at him, and John cringed from the rage in his eyes, he couldn’t help it.

“I’m sorry,” he babbled immediately. “I’m so sorry, I did try to stop him,” and he wasn’t sure if he was apologizing for the attempt or its failure. McCoy took a deep breath and knelt in front of him, lifting up his head and thumbing back his eyelids to check his pupil response.

“Get out,” he said, not looking behind him. The captain didn’t move and McCoy turned his head. “I said, get _out_. The both of you.”

“His mind,” Spock said, “It’s-“

“I’m not talking to you right now, Spock. Take a fucking headache tablet if you want.” He turned back to John. “Are you okay?”

“The things he showed me-“ Spock started, and McCoy whirled to face him. For a moment John thought the doctor might punch him again, but-

“If you didn't want to see bad things, you should have thought twice before you invaded a rape victim's mind, Spock. You knew what he’d been through and that should have told you _everything you needed to know_ about what you’d find in there. But no, you just had to go ahead and rape him again, didn’t you? How’s those Vulcan ethics working out for you?”

John had never seen a Vulcan look horrified before.

“I didn’t-“

“Look up the definition, Spock. For now, though, get the _hell out of my sickbay_.”

The captain and first officer scuttled out, chastened, and McCoy turned back to John. He helped him sit down on the examination table. John’s entire body still tingled from the tangle field, and his legs were shaky and uncertain.

“Did he hurt you? I know unwilling melds can be painful, do you need some painkillers?”

John stopped him, taking one of McCoy’s hands in both of his.

“You don’t have to worry, Doctor,” he said gently. “I didn’t let him see what you told me.”

“You…what?” McCoy looked stunned. “You think I was angry because he found out what I’d been? John, I was angry because he _hurt_ you, and because you’re in my care. He should never have done that, and believe me, I _will_ be telling his father about it. I didn’t know you could keep things from a meld, though.”

“You can’t,” John said quietly. “But you can...distract them. I showed him things he didn’t want to see, so he stopped looking.”

McCoy’s face was doing something complicated now, and John couldn’t read his expression. There was still anger there, but mostly there was a kind of wonder, and a deep, deep sadness. Of course, McCoy would know what it had cost John to throw his humiliation in his rapist’s face like that.

“Oh, you brave, wonderful man,” McCoy said, and folded John into a hug.

The praise lit a warm fire in John’s heart, and he rested his head on McCoy’s shoulder and allowed himself to take the deep, shuddering, sobbing breaths he’d been holding since McCoy came in like the hammer of the gods.

And McCoy held him while he cried.


	7. Chapter 7

 

When Khan eventually settled down, Bones commed Uhura. She was down in Sickbay a few minutes later, a worried expression on her face.

“Doctor? You said something was wrong?” she asked. She’d glanced at Khan when she came in, but seemed completely unfazed by the augment’s presence in Sickbay. Of course, she’d heard the scuttlebutt. Knowing her the way he did, Bones would not be at all surprised if she hadn’t been keeping an eye on them through the security system.

“We may have a bit of a problem, Nyota,” he said. “Can you think of a place between our current location and Earth where we can safely stash seventy-two torpedoes? Without it showing up in the logs at all?”

“The special long-range ones Admiral Marcus gave us?” she asked. “Why?”

“Because if we go to Earth carrying them we’ll be arrested on the spot. I can’t go into details right now, but suffice to say that if we’d fired those torpedoes at Qo’noS we would have been guilty of genocide.”

“In more ways than one,” Khan said, and Bones turned to him. The augment looked at him with wide, red-rimmed eyes. “My crew are in those torpedoes,” he added. “We’re the last of our kind.”

For a few moments, Bones lost the ability to speak. For Khan to do that, as broken as he was, as _watched_ as he was…dear God. It should have been impossible, just like diverting a mind meld the way he’d done should have been impossible.

“You did that?” Uhura asked. Her voice was as filled with admiration as Bones’ mind, and Khan smiled a little. Of course Uhura would understand the accomplishment those torpedoes represented, the sheer magnitude of the miracle Khan had apparently wrought.

“I was going to take them and run,” he said. “Before my Lord Admiral convinced me that I shouldn’t.”

Uhura looked between them, then sat down.

“Doctor McCoy, please get Chekov and Sulu for me. Now, you. Um...” she looked at Bones.

“He prefers to be called John Harrison,” Bones supplied, and turned away, keeping half an ear on their conversation.

“Okay, John. Those torpedoes, we’re going to need some more specs on them soon, but I need to know if they’re trackable. If we dump them in space, are they going to start screaming bloody murder for someone to pick them up?”

Khan sat forward in his seat and started talking animatedly, clearly put at ease by Uhura’s no-nonsense attitude. By the time Bones had gotten off the comm with Sulu, Uhura was sitting next to him, and by the time he’d gotten Chekov to agree to come down for a check-up, they were drawing on the same datapad.

“I can fudge the logs,” Uhura said when the others had arrived. He was scowling at Khan, who was subtly withdrawing again, refusing to meet anyone’s eyes, his long fingers plucking at the hem of his shirt. “But you, Hikaru, need to find us a place to stash these where we don’t have to divert more than an hour or so. Chekov, you need to find an excuse for us to drop out of warp so that we can dump them, and rig up some kind of container for them.”

“Does the captain know about this?” Pavel asked nervously.

“Not as such,” Bones admitted. “We’re going to present them with a  done deal and let them cope.”

“There’s an ugly word for that kind of thing, Doctor,” Sulu said. ‘It rhymes with … it rhymes with something that rhymes with mutiny. Okay?”

“It’s not mutiny,” Uhura said. “It’s protecting Jim and Spock from their charming overabundance of faith in the wisdom of the Admiralty. They no doubt believe that if they tell Starfleet Command that the torpedoes were assigned to the Enterprise by Admiral Marcus – something of which there’s no record, by the way, which was one of the things that pissed Scotty off -  Starfleet Command is going to say something along the lines of ‘sure, they’re nice boys, let’s believe them’ instead of throwing the entire crew in a deep dark hole for all eternity.”

“Not to mention,” Bones said, “if those torpedoes fall into the wrong hands it would be very, _very_ bad.”

“But Starfleet-“

Bones surprised himself by laughing bitterly. Sometimes Bones envied people like Jim and Hikaru and Pavel; people who’d never had to see the dark side of Starfleet, the cancer at the heart of the Federation. Other times he thought they were unforgivably stupid for not seeing something so blatantly obvious.

“Oh, boys,” Uhura said. “You have _no idea_. Starfleet command is _exactly_ the wrong hands. Nobody should have that kind of power. Nobody at all.”

 _But especially not Starfleet admirals_ was unspoken but understood, at least by Bones.

“Now,” Nyota said briskly, and shifted so that she was sitting in front of Khan, shielding him a little from Sulu’s stern look of dislike. “Shall we begin?”

**Notes for the Chapter:**

> Short update because I'm technically too busy to be writing fic right now.
> 
> I hope everyone else loves Uhura as much as I do, because I have a feeling we'll be seeing a lot more of her.


	8. Chapter 8

Once the meeting was over and everyone scattered to do their bits, Bones settled down to do his paperwork, giving Khan some reading to do. The augment had done remarkably well in the meeting, even volunteering some information, and by the end had almost shifted entirely out from behind Uhura.

“Your Lieutenant Uhura,” Khan said eventually. “She’s…unique.”

Bones smiled to himself.

“That she is. Strongest person I know, John. There isn’t another like her in the world.”

Khan nodded and settled down with his back against the wall, his knees pulled up to his chest so he could balance the datapad on them.

“It’s fascinating, seeing how they broke me,” he said. “I would have thought it would be upsetting but it’s…comforting. Knowing that I’m not the only one this has happened to.”

“I’d have liked the same comfort when I came out,” Bones said. “Unfortunately, nobody who worked with me had the…let’s call it benefit of experience, that I have. If it’s any comfort, what you endured would have killed anyone else. They probably had an absolute bitch of a time with you, didn’t they?”

Khan laughed softly, and Bones marked it as a triumph.

“That they did. My Lord Admiral nearly gave up on me several times. I nearly killed him, the first time he touched me.” Khan leaned his head back, smiling with a kind of quiet pride Bones could understand only too well. Once you’ve been broken, once you’ve surrendered the last vestiges of self to another, the only thing there was left to take pride in was how hard you made them work for it. And Khan had made them work _incredibly fucking hard_.

They worked in silence for the rest of the shift.

There was, inevitably, drama once the redshirts figured out that Bones wasn’t taking Khan back to the brig.

“I don’t care what your orders are, Ensign,” Bones eventually said flatly. “The last time I left my patient in your charge you allowed him to be _assaulted in my sickbay_. So he will be sticking to me. If that means that he spends the night in my quarters, then so be it. You can just suck it up and set up station outside my quarters. Are we clear?”

“Sir, we-“

“Are we _clear_ , Ensign?” Bones asked, making his voice as soft and deadly as he knew how, and felt Khan shudder where he was pressed against Bones’ back.

The ensign – poor boy probably didn’t deserve this, he was just trying to do his job, but fuck if Bones cared – paled, gulped and nodded, and his entire detail fell in meek as anything behind Bones as he strode to his quarters.

The moment the door closed behind him Khan went to his knees, his eyes on Bones’ face as his hands went to his trousers.

Bones slapped them away.

“For Gods’ sakes, Khan, this is _not_ why I brought you here!”

Khan rested his hands on his thighs and looked up at him with wide blue eyes, his tongue flicking out to moisten his bottom lip.

“I know that, Doctor,” he said quietly, his rasping voice a full octave lower than usual. “But I want to _thank_ you. For everything you’ve done, everything you’re doing. I want to please you, won’t you let me?”

And damn if the man didn’t beg as prettily as any whore, eyelashes making a dark fan on his pale cheeks, his voice a bare whisper by the end. His one hand reached out, stroking up Bones’ thigh gently, almost but not quite touching the bulge where Bones was hard as a fucking rock, because there was nothing quite like having a beautiful man on his knees.

It took more fortitude than Bones had ever thought he’d possessed to cover that wandering hand with his own, lean down and tip Khan’s face up to his.

“You don’t have to thank me,” he said firmly. “I’m not doing this for thanks, and even if I were, sex isn’t the way to pay me back. Okay?”

Khan nodded, his expression open and vulnerable again, without the sweet begging artifice he’d no doubt learned at Marcus’ feet.

“But how can I thank you, then?” he asked.

“By getting better,” Bones said firmly. “Now, see if you can figure out the kitchen, I need a shower.”

By the time Bones emerged, feeling much refreshed and incidentally slightly wobbly in the knee department, Khan had produced an actual dinner (well, it was beans on toast, but Bones wasn’t about to argue) for Bones, and a protein shake for himself. He’d managed almost an entire biscuit at lunch, but his main sustenance was still the shakes.

“The couch is comfortable enough,” Bones said as he shovelled food into his mouth. “I’ll get you some extra blankets, you’ll be fine. The door’s locked from the inside, and nobody can come in, so that’s all sorted. Yes? If you don’t want to sleep, there are headphones for the viewer, you can catch up on popular culture. Don’t wake me until morning, or unless you’re on fire. Okay?”

Khan nodded obediently.

Of course, Bones didn’t get an uninterrupted night of sleep. Because the gods hated him. He’d barely nodded off when Khan was shaking him, holding a finger to his lips and pointing at the vent access. Now that he was  (dammit!) awake, he could hear the soft thuds and thumps of someone making their way through the vent shafts.

Bones sighed.

“Don’t worry, it’s nothing you need to be concerned over,” he said, and took off the vent cover (kept in place with magnets, the screws just for show) just as Uhura reached it. She unfolded herself with a lanky kind of grace, looking not at all like her usual self in a nightdress, with her hair in a loose cloud around her head and tear-tracks on her face.

She was still shaking – a bad one, then.

Bones didn’t say a word, just opened his arms and let her fall into them, sobbing. He murmured soothingly to her and met Khan’s eyes over her head. The augment had clearly gone through puzzled and into understanding in record time, and tipped his head enquiringly as he reached out and laid a gentle hand on Uhura’s back.

Bones reached around and pulled him against her, and they stood there making a little cocoon around her until Uhura’s breaths eased and she lifted her head.

“Sorry,” she muttered, wiping her eyes. She always said that.

“You don’t have to be sorry,” Bones said, as he always did. “I’ve gone to pieces on you more than enough times.”

“You don’t have to be ashamed of the aftereffects of trauma,” Khan rumbled, the bloody great hypocrite. Uhura laughed softly.

“Can I stay here tonight?” she asked, and Bones nodded without hesitation.

Ten minutes later they were all on the bed together, Uhura’s head snugged under his chin and Khan pressed up against her back. It brought back memories.

“Do you remember Estelle?” Uhura asked into the quiet, and Bones nodded. He remembered every single person who’d spent time in the pens with him. Most of them were dead now – as far as he knew, only Nyota and himself remained. “She used to have the worst nightmares, John. She’d wake screaming and we’d all have to snuggle up to her just like this, and Bones used to gag her so that nobody could hear. She lasted only a few months, then she didn’t come back.”

There was more to it than that, of course, but he had been seventeen and Nyota (although of course she’d had a different name then) had been only ten, and there was no way to tell someone who looked at you as though you’d hung the sun and moon (despite everything that happened outside the slave pens, despite everything you’d done) that you’d murdered her best friend, even if you hadn’t wanted to, even if your hands had shaken so badly that you’d screwed up the first few cuts until your Lord Commander had taken your hands in his and guided them.

“There was nobody else, when I was there. My Lord Admiral said that he’d had to send all his other pets away because I’d have hurt them. I think he had them killed.”

“Not your fault,” Uhura murmured.

“Can I ask you a question?”

She nodded.

“Did he give you your name too? It seems like a strange name to give a slave, Uhura.”

Bones laughed softly and put a hand on the back of Khan’s neck.

“No, he didn’t,” he answered for her. “Remember how I told you that she was the strongest person I knew? When we got out, I didn’t have a name that I could remember, so I kept the one he gave me. But this one, this one spent weeks looking through books until she found a name that she liked.”

“Nyota means star,” she said sleepily. “And Uhura means freedom. And now I’m free among the stars. My name was a promise to myself.”

“Maybe,” Khan said softly. “Maybe when I’m better, you can help me choose a new name.”

“I’d like that,” Uhura said just as softly, and that was the last Bones knew before he drifted into sleep.

**Notes for the Chapter:**

> So apparently everyone on the Enterprise has sekrits. Who knew?


	9. Chapter 9

John woke slowly, surrounded by warmth, with Uhura’s long dark hair tickling his nose and McCoy’s muttering coming from the tiny kitchen area where he was apparently cooking something. That’s what John’s nose said, anyway, and it was almost never wrong. It was hard to mistake the scent of frying bacon for anything else, anyway.

He contemplated getting up for a few seconds, but then Uhura shifted and laid her head on his shoulder, murmuring sleepily.

“’time is it?” she asked.

“Just after five AM,” he said, grateful for the return of his internal clock. It had gone haywire under his Lord Admiral’s care, although at the time he had been convinced that he had just been mistaken, been wrong.

“Mmm, I can stay here for a bit longer, then,” she said, and pulled the duvet up over her shoulder, her eyes drifting closed.

“Nyota,” he said softly, “how do you do it?”

“Do what?”

“Trust,” he said simply, and it was the hardest question he’d ever had to ask. Even now, even here with McCoy who had never hurt him, had _struck a superior officer_ in his defence, it had taken hours to fall asleep, and he couldn’t imagine being like Uhura, sleepy and warm and trusting in his arms, ever again. Not that he’d ever been this soft, but…

“It wasn’t easy,” she said finally. “You have to make a decision. I decided that if I let them touch the rest of my life, that was letting them win. So I worked at it, at being more trusting, at letting myself relax around strangers. Not that you’re a stranger. You’re my brother, after all. Now hush and let me sleep a bit more.”

He did, ignoring the prickle of tears in his eyes. It was such a simple thing, but… _brother_. All his brothers and sisters were asleep, still unaware of the danger they found themselves in, but he was coming around to the idea that there was more to family than biology, more to strength than just the physical. And if he came away from what had happened, what had been done to him, with a new family, that was something, at least. And nobody could argue that Nyota, who had been through so much and refused to let it stick to her, was not strong, or that McCoy, who fought the desires he’d learned in the hardest ways every day - and John could _see it_ , could see the way McCoy looked at him whenever he obeyed unthinking, see the way McCoy fought down the urge to see what more he could take, what he could order John to do (anything, McCoy could order him to do _anything_ and he would obey, would obey with a glad heart) – was anything like weak.

He must have fallen asleep, because the next thing he knew was McCoy’s gentle hand on his shoulder, shaking them both awake. There was an odd expression in the doctor’s eyes, something almost sad, but his face was smiling.

“Come on, sleepyhead, time to try some solids again!”

John’s stomach clenched at the thought, at the memory of his humiliated vomiting at their last attempt, but McCoy just smiled and Nyota squeezed his shoulder, and somehow he found the courage to sit at the little table in McCoy’s kitchen unit and allow the good doctor to put a plate of scrambled eggs in front of him, with a single strip of bacon.

Nyota sat down next to him, studiously ignoring him, and tucked into a much larger portion.

“Try it,” she said around a mouthful that really shouldn’t have fit in her actual mouth, “it’s delicious.”

So he took a careful bite of the eggs, rolling it around his mouth until it was barely recognizable as a solid, and then swallowed.

His body was not fooled. His stomach roiled and for a moment he thought he was going to be sick. But the feeling subsided and after almost a minute, he risked a bite of the bacon.

Before he knew it, the entire plate was empty, not even a crumb remaining, and John found himself actually worried for the structural integrity of McCoy’s head. Surely nobody could actually smile that widely without damaging something?

The doctor shoved a shake at him anyway, and when John raised an enquiring eyebrow, he shrugged.

“That wasn’t enough to feed a bird, kid, and you know it. Now drink up, you’ve got a lot of mass to get back.”

John might have said that he’d already picked up four kilo’s under McCoy’s care, but he didn’t. He was still hungry, after all, and nobody here was going to call him a greedy pig because he needed more nourishment than a normal human. Though looking at the pile of food Nyota was packing away, he was beginning to doubt that assertion.

She caught him looking and shrugged an elegant shoulder.

“They did some work on me, when I was little,” she said. “It turns out that if you add nanites to a child’s bloodstream they build little colonies all over the show. Upside, a lot of additional processing power and memory storage, and the ability to directly interface with most modern computers. Downside, the kind of appetite that sumo wrestlers look cross-eyed at.”

“They experimented on you?”

“On all of us. That’s what the Starfleet Youth Development programme was supposed to be about, after all,” McCoy said. “Well, not technically. But you put a bunch of scientists and a man like Alexander Marcus and a group of gifted youngsters in a remote station…inquiring minds are going to find uses for their time. Personally, I was enhanced for medical work. Entire medical library, right here in my brain, micromuscular augmentation in my hands – they have to be steady for surgery, after all – and a bit of extra oomph in my eyes, because isn’t a doctor who can take your temperature by looking at you _useful_?”

Khan had opened his mouth to say… _something_ , he wasn’t sure what, wasn’t sure what he could say to the note of bitterness in McCoy’s voice, when something beeped and Nyota blinked three times in rapid succession, her eyes flashing blue.

“Shit,” she said. “Spock’s looking for me. See you boys later.” And with a quick kiss to each of their cheeks, she shimmied back into the vent she’d appeared from and was gone.

“So,” John said after a while. “What are we going to do today?” It was the last possible time to dump the torpedoes – they’d be entering the Sol System in just over eight hours, and he was fidgety. They still had no clear plan on what was going to happen once they reached Earth, although John suspected he would be made to testify against his Lord Admi- against _Admiral Marcus (ignore the pain, it’s just a memory, he’s not here and he can’t hurt you)_ and then…something. Back to the Enterprise with McCoy? He couldn’t really picture it, but where else was he going to go?

“We,” McCoy said, leaning back in his chair, “are going to do…absolutely nothing. It’s all down to Nyota’s little electronic minions, and Sulu and Chekov, now.”

‘Nothing’ lasted for an hour, until John got restless with worry and McCoy decreed that they were going for a walk. So they strolled out into the corridor – McCoy nodded at the redshirts with a pleasant smirk – and went for ‘a walk’. John tried not to crowd the doctor, but it was hard, hard not to flinch from every person they passed, hard not to stare at his feet (still bare, McCoy’s shoes didn’t fit his much larger feet) whenever he caught a look of disdain thrown his way.

To his surprise, McCoy took his to the quartermaster, and had him swop his comfortable sweats for a grey Starfleet uniform, without rank insignia or communicator, and a pair of soft shipshoes. Then he took him to a small room where a man (did they really have _barbers_ on Starfleet vessels?) gave John a haircut, trimming his too-long fringe and in general neatening his appearance. He thought about protesting, but the raggedly trimmed ends where his long locks had been sheared away were disgusting and annoying, and a proper haircut would allow his hair to grow back more neatly.

“There,” McCoy said when they were done. “Now you look a bit more respectable.” John had to agree. He still didn’t look like _himself_ , not by a long shot, not in this bland soft uniform and with his hair short. But at least he didn’t look like a refugee or a slave anymore, and that was something.

Leaving the barber’s rooms, John bumped into someone. He looked up to apologize…and froze.

The blond woman’s face twisted into an expression of fear, and she took a full step away from him.

“ _You_ ,” she snarled, and John reached for every moment of strength he’d ever had, and managed not to fall to his knees.

“Doctor Marcus,” he said quietly. “Does your father know you’re here?”

It was a good thing that McCoy was there, because John could not have caught her as she fainted. He couldn’t have laid a finger on her for all the money in all the worlds. Not again.

**Notes for the Chapter:**

> Today, I am sad, because my brother is going to New Zealand and I won't see him for a long, long time. So I wrote some schmoopy fluffy things and gave Khan a haircut to make me feel better.
> 
> Next chapter: What happened between Khan and Carol? How is Khan going to react to seeing Admiral Marcus again? Shit's getting real, guys!
> 
> Also, I don't know if reboot verse have barbers. I know that there was a barber on the Enterprise-D. He was blue, and fabulous, and suddenly I needed him on the Enterprise. Because reasons.


	10. Chapter 10

**Notes for the Chapter:**

> Short little update because it's Saturday and I love you all.

Bones looked down at the unconscious woman in his arms – _Doctor Marcus? Not…not Carol Marcus, Jesus fuck Leonard you’re just the king of Thicktown this week aren’t you?_ – and back at Khan, who was backed up against the wall, his arms wrapped tightly around himself and his eyes closed.

“A little help here?” he asked, but Khan shook his head frantically and looked like he was trying to dig his way through the bulkhead with his shoulderblades, so Bones cocked his head at a redshirt who moved to take not-doctor Wallace from him. She was already starting to stir, but she closed her eyes and let herself lay limp, waiting for them to arrive in Sickbay, where the redshirt lay her down on a bed before retreating far away from the CMO and all the weirdness surrounding him, before she sat up and rubbed her hand over her face.

“Doctor McCoy,” she said softly, but her eyes were fixed on Khan, who was hovering near the door, his arms still wrapped around himself and shaking so hard Bones could see it from where he was standing.

“Carol. You’ve changed your hair.”

She smiled bitterly and touched the severe bob her hair was in, so different from the long dark tresses of their shared childhood. Her eyes were different too, or perhaps that was just because she was wearing different make-up – the things women could do with the stuff never ceased to amaze him.

“He insisted, said you’d recognize me if I kept my own hair,” she said. “You know why I’m here, of course. I was to make sure those missiles were fired. He’s going to be…upset.” She didn’t look worried, but Bones had known her long enough to know that she was a fucking amazing actress, when she wasn’t surprised by what he could only assume were unpleasant memories.

“And I assume you know…my friend over there?”

She nodded.

“John,” she said, hopping off the table and going over to him slowly, her hand stretched out ahead of her. He didn’t flinch, just barely, but his eyes closed and the expression on his face was almost one of pain as she touched his arm. “John, it’s just me. Just Carol. You’re okay, you’re safe here. John, please look at me?”

He opened his eyes and stared at her in disbelief, his mouth half-open.

“I’m okay? _I’m okay_? Oh, God, how can you even think about me when I…you should have me thrown in the brig, you should…oh, god, _Carol_ , I’m so sorry, I failed, I’m…” the rest of his words were lost in a torrent of sobs as he turned away from her and pressed against the wall. Bones hurried over and pulled him away, pulling the taller man into a firm hug.

“Someone please explain to me what the hell is going on here?” he asked in what he thought was quite a reasonable voice. Apparently he failed, because Khan cried harder and Carol frowned at him.

“I’m sure you can deduce it, Doctor,” she said coolly. “I upset my father, he used John to punish me. It was a valuable lesson for both of us, I think.”

And realization dawned suddenly.

“Was it ‘be good and nothing will happen to her?’” he asked.

“It was the usual routine,” she said drily. “He had me bring him food, help him eat – that was while he didn’t have his arm, I think he tried to punch Daddy. I tried to warn him, just like I tried with you. It worked about as well. Damn men anyway, you’re too fucking sentimental. He got attached and Daddy saw, so…showtime.”

“Stop trying to defend me,” Khan said quietly, stepping out of the hug. He didn’t look at Carol’s face, kept his eyes trained on his feet. “I _hurt_ you.”

“Not by choice. And you did try, John. You tried so hard,” she paused to swallow. “Nobody’s ever tried that hard, it’s not your fault it didn’t work, okay?”

Khan shook his head, but froze when Bones lifted his chin and forced him to look at him.

“John, if I’m right about what happened, the exact same thing happened to me. He told you if you did…something, and did it well, it doesn’t matter what it was, then nothing would happen to Carol, and she’d be fine, yes? And then you did it and he said you hadn’t been good enough so he hurt her.”

“Not personally,” Carol said. “I’m too old for that kind of thing now. No, he made John do it. Useful little thing, control chips.”

Well. Well, that just put a fucking bow on everything, didn’t it? Bones looked from her to Khan, who was back to staring at his feet, and ran his hand through his hair.

“Well, that’s just fucking brilliant, isn’t it? I have to hand it to your father, Carol. He’s a fucking master of mind-games.”

“He is at that,” she said sadly. “It’s really amazing the way he can always tell when I really like them. I mean, sometimes I even manage to fool myself, but never him. I really do like you, you know, John. You tried very hard, but you were never going to win. Nobody ever does.”

“We might,” Bones said as the ship shuddered around them – Chekov’s malfunction, right according to schedule – and dropped out of warp. “I think I’ve had just about enough of him. What do you say, Carol? Care to join John and I in taking your father down?”

She smiled softly, sadly.

“You’re not the first to think you can do that, Bones. What makes this time different?”

“This time, I have a Vulcan witness of impeccable character ready to submit to a mind meld to render testimony against him, obtained via mind meld with one of his victims. I have a respected medical man – that’s me, by the way – willing to testify that Alexander Marcus tortured and abused a prisoner in his care – that’s you, Khan, oh, don’t flinch. I have a Starfleet captain who’s going to tell the world that Marcus ordered him to fire a torpedo at the Klingon home world. And best of all, I have Nyota Uhura, and she’s on the warpath.” Bones didn’t miss the way her face slowly brightened as he told her his list, the bare bones of the plan that had been percolating through his mind ever since the first time he saw Khan. “What do you say, Carol? Want to add that we have his daughter ready to testify about years of systematic abuse and torture?”

Her smile was as brilliant and vicious as he remembered it.

“Oh, _yes_ ,” she breathed.

**Notes for the Chapter:**

> dooom dooom doom doooooooom.
> 
> So, that's what happened with Carol and Khan.
> 
> I'm going to assume that Spock and Jim talked to Bones while Khan was asleep in the previous chapter. Might do a missing scene for that once I've finished this.
> 
> Next up: Admiral Marcus shows his slimy face, and is made sorry.


	11. Chapter 11

**Notes for the Chapter:**

> Sorry for the delay. I quit smoking. It's not going well.

Exactly thirty minutes after the ship dropped out of warp, the engines whined up again and they were off. Not that John cared. He was lying on McCoy’s cot, his head in Carol’s lap as she stroked his hair, listening with half an ear as she discussed McCoy’s plan, the British accent she’d affected before nowhere in sight.

He wasn’t particularly interested in the plan. He’d do his part, testifying and all that, but if he had to be honest, he didn’t think it was going to work. Take down the Admiral? As _if_.

He was proven right less than an hour after the Enterprise entered the Sol system, when the ship was jerked roughly out of warp, setting the gravity flickering long enough to hurl him to the floor. The lights flashed red as the ship went to Battle Stations and John, fighting panic, grabbed McCoy by the arm.

“What do I do?” he asked. McCoy put a hand over his and grinned fiercely.

“Just stay calm, everything’s going to be okay. Okay?”

John nodded and went to sit down on the cot again, next to Carol. She had a strange look on her face.

“You okay?” he asked.

“He’s brought the Vengeance,” she said. “How can he have brought the _Vengeance_?”

“But it’s not ready yet! Won’t be combat ready for months yet!” he said. “How can he have-“

“Well, he’s clearly got the warp grapples working,” she replied. “Bones! Tell Jim to stop trying to fight it, this ship’s not going anywhere!”

McCoy cast them a glance and relayed her advice, and a moment later the frantic whine of the engines calmed slightly.

“You know what we’re up against?” McCoy asked, coming over to them. “Explain.”

John gave him a summary, quick as he could. The _Vengeance_ , the Admiral’s pet project. How he’d made John design it, supervise the work on it.

“What are its weaknesses?” McCoy demanded. “Jim says they’re demanding we submit to arrest, can we fight it if we have to?”

“It doesn’t _have_ any weaknesses,” Carol snarled. “It’s the perfect ship, Bones. John designed her, and I checked him every step of the way with Daddy hovering over my shoulder like a fucking vulture. Even if we wanted to, we couldn’t have done a damn thing to it. We have to surrender. There’s nothing else to do. He can blow us out of the sky with the press of a button and cover it up however he likes.”

 _Surrender_. John shuddered at the thought, and McCoy must have noticed because his expression firmed.

“Not on your life, Carol. Come with me, both of you.”

They followed him meekly to the bridge, dodging frantically running crew on their way.

John noticed the captain and first officer turning towards them as they entered, and then he saw nothing but the face on the viewer, vast and terrible like the god he’d seemed all those long months, and he found himself on his knees without knowing how.

“My Lord Admiral,” he whispered, and it sounded reverent to his own ears, the whisper of a penitent hoping against hope for mercy. He hated himself for it – he’d been doing so _well_ , only a few more weeks, a few more _days_ with McCoy and his kind hands and gentleness, with Nyota’s bright example to follow, and he might have been able to face the man on his own two feet. “My Lord Admiral,” he said again, and he didn’t miss the way McCoy turned to him, or the way Nyota dropped her head into her hands.

“John,” he said, quite calmly, almost kindly, and a shudder went through him hearing that voice again for the first time in so many weeks. “I see they found you after all. Excellent. Take them into custody.”

The bridge went deadly silent and John looked around, at the crew who hated and despised him, at Nyota and McCoy and Carol who’d been nothing but kind, and felt his muscles tense in preparation, in instinctive obedience. He could do it, he _would_ do it, overwhelm them with his augmented strength, deliver them to his Lord Admiral bound in ribbons. He shouted down the voices of dissent, the ones that screamed of betrayal and pain to come, and rose to his feet. He hit the ground a moment later, the buzz of a tangle field his only clue, and looked up at McCoy, who was kneeling at his side with a gentle smile.

“I’m not an idiot, John,” he said, stroking John’s hair. “I’m sorry about this.”

And John couldn’t move, couldn’t give voice to his desperate gratitude as the doctor turned away to face the admiral.

“I don’t think so, Sir,” Kirk said.

And John could hear the cruel smile in the admiral’s voice as he said, “very well then,” and fired.

The _Vengeance_ ’s weapons were stronger than the _Enterprise_ ’s shields. They were stronger than any shields in space; John had designed the focussing arrays for the phasers himself, had calibrated the loads for the torpedoes personally, late nights in the weapons labs with no company but Carol or his own thoughts, physical pain pushed to the back of his mind and not thinking about anything but pleasing his Lord Admiral.

The _Enterprise’s_ shields held for all of two volleys, and then they flickered and faltered and the ship lurched, and John heard his Lord Admiral laugh as he was beamed away.

**Notes for the Chapter:**

> Pretty sure there's only one chapter left and then the epilogue.
> 
> The next chapter is not going to be pretty, y'all.


	12. Chapter 12

John came back to consciousness in a startled flash. He would have sat up, if he could have, but his body wasn’t responding. He couldn’t hear the tangle field, so what-oh.

Oh, of course, and now that he was properly awake he recognized it, recognized the weight around his neck and the feeling of numbness in his limbs.

“John,” someone whispered. “Open your eyes, please.”

He obeyed, already lost in the almost comfortable despair of slavery, and looked around. The first thing he saw was Nyota, an agonizer collar like a blasphemy against the smooth skin of her neck. They were all here; McCoy and Uhura and Carol, and even the captain and the Vulcan – John didn’t look too hard at him. The captain and the Vulcan were collared, chains leading to the wall of the pen, but McCoy and Carol wore collars like his, not chained to anything but unmoving.

“What happened?” he asked. “How did you all…”

“Well, we had to surrender once he had the shields down, didn’t we?” the captain said bitterly. “He could just blow us out of the sky if we didn’t.”

“I’d have let him,” Carol muttered, her face almost comical where it was squashed against the grating that made up the floor of the pen. She would have marks there, a crosshatch of red lines on her face and the bare skin of her body. “Be better than this. And he’s just going to kill you all anyway.”

“Eventually,” Nyota said. “Don’t be so negative, Carol. While there’s life, there’s hope.”

McCoy’s chuckle was bitter as acid, and John just closed his eyes. There was a time for hope, and there was a time when hoping was pointless, would only make it hurt so much more. This was that time. The only bright spot that he could see was that his crew, his blood-family, was safe as they could be, floating in space. They’d never wake, but in the world as it was now, perhaps that was a good thing. At least they were safe.

The pen’s door slid open and if he could have moved, John would have cringed. But he couldn’t, and so he just lay there, waiting for his Lord Admiral to call for him.

It didn’t take long. A second later he could feel his arms and legs again, still half-numb and rubbery but under his command again, more or less. He didn’t wait to be ordered – it was never a good idea to make the Lord Admiral wait – just rolled over and crawled to the door, his head brushing the roof of the pen. Outside, he went to his knees, his eyes fixed on the gleaming boots in front of him.

Carol was next, and she knelt close enough that the warmth of her skin stole some of the cold from his body.

“Carol,” her father said. “I’m disappointed in you, my dear. You know you’re going to have to be punished for this.”

She said nothing, but from the corner of his eye John could see her chin lift, and he imagined he could see the fire in her cool blue eyes. He didn’t quite understand her defiance, although he admired it. What use was there in provoking their master even more – and John knew, could tell from the tone of his voice that his Lord Admiral was in a killing rage –, what did it benefit? A slave had no use for pride, unless it was pride in being a good slave, but John had never managed that.

There were a series of ragged gasps and moans from inside the pen and McCoy and Uhura came tumbling out, gasping. Resistance again, he thought, and closed his eyes because Nyota’s ragged pained gasps hurt something inside him. She shouldn’t be here, shouldn’t be in this place. She should be as free as her name.

“Fetch your captain, Leonard,” the Admiral said. “And the Vulcan. Warn them what will happen if they try anything.”

McCoy turned wordlessly and crawled back inside. There was a short discussion, McCoy’s sharp impatience eventually winning over the captain’s anger and the Vulcan’s cool logic, and he came crawling out again, leading Kirk and Spock by their chains. It amused John to note that they tried to avert their eyes from all the skin on display. They’d learn.

“Marcus, what the hell-“ Kirk’s words were cut off as Nyota crumbled with a gasp, bowing until her head touched the ground. “Stop! Stop it!” he cried, and tried to lunge for her, but McCoy’s grip on his leash kept him in one place.

“Just shut up, Jim,” he said dully. “It’ll be over soon.”

“Very good, you remember,” the Admiral said. “You talk, she hurts. It’s a simple equation, Jimmy, even you should be able to understand it. Now, everyone follow me,” he said, and turned and walked away.

They followed, Carol and John helping Nyota to her unsteady feet. Her hand clenched around his arm like a claw, and he looked down at her.

“When I say the word,” she breathed, softly enough that the sound of their passage almost obliterated her voice, “you need to move.”

“Nyota, I…”

“Can you do this for me, Khan?” she asked.

“You’re the only one who can,” Carol murmured from the other side of Uhura, “can you do it?”

“I…” he paused. Nyota was terrified, he could feel it through her skin. But _she_ was still thinking. She was thinking and planning, her and Carol both, while he was numb with fear and despair. He couldn’t _not_ try. “I can try,” he whispered back, and she squeezed his arm and smiled shakily.

“Good. Good. Wait for my signal.”

They followed the Admiral to his quarters, a row of cowed ducklings following the leader. There, McCoy chained his glaring captain and the first officer to the wall before joining them kneeling near the door.

***

He needed to _think_. Bones needed to think, because he’d gotten them into this mess and there was a way out, there was always a way out, now if only he could _find_ it, but his mind was slow with the remnants of drugs – his enhancements helpfully informed him of the exact components of the cocktail they’d been gassed with – and he was so _afraid_. Jim was glaring at him from across the room, chained neck and ankle to the wall with a ball gag stretching his mouth, and Bones understood, he really did, how betrayed his captain probably felt. But there was nothing to be done.

Marcus paced in front of them and Bones could just barely get up the courage to look at his knees, but there was no way to still his shaking hands. They stopped, though, as soon as the collar activated again, divorcing him from his body and leaving him floating.

“Falahi,” Marcus snapped, and Uhura tensed. “Come over here. And you, John. You’re going to put on a little show for me.”

Uhura and John – Bones couldn’t think of him as Khan in this place, could just barely hold on to the name Uhura had chosen for herself – crawled to the centre of the floor, where they knelt patiently.

And then, suddenly, Uhura snapped out ‘ _Now!’_ and John/Khan _moved_ , and Jesus, Bones had seen enhanced humans move before, had had some inkling of what Khan might move like from the way he slithered about as though his bones were liquid, but he had never expected _this_.

He’s never expected to see Khan go from kneeling to standing in a single sharp motion, his hand coming up to slap the controller out of Marcus’ hand even as he punched the Admiral in the face. Nyota collapsed at Khan’s feet and Carol screamed but he paid them no mind as he backhanded the Admiral across the room.

“John,” Marcus cried, forcing the words through his ruined mouth, spitting blood. “John, _think_ about what you’re doing!”

John Harrison strode across the room like an avenging angel, light catching and gleaming on his scarred pale skin, and hauled his Lord Admiral to his feet with a hand on either side of his head.

“My name,” he gritted out, the muscles in his arms and back bulging and straining with effort, “is Khan.”

His last word was drowned out with a sound like a coconut falling and he let go, staring at his bloody hands as though he couldn’t quite believe what he’d done.

Bones couldn’t spare a moment to stare at the bloody ruin of his former master’s head, because Uhura and Carol were beyond screaming now.

“Khan!” he yelled. “The remote!”

His voice seemed to snap Khan out of his daze and he dove for the remote, fumbling for a minute with bloody hands until he managed to turn it off, and the girls relaxed, gasping for breath. A moment later they were both on their feet, more resilient than Bones who was still trying to make his knees obey him, but they pulled him to his feet and they stood, staring.

“He looks so _little_ ,” Nyota said, padding closer almost timidly, almost as though she expected him to come back to life (not bloody likely, not with his head crushed like a fucking melon). “Oh, Khan, you _killed him_.”

Khan backed away from her but she wasn’t having any, she flung her arms around him and laughed wildly, kissing him all over his shocked face.

“Oh my god,” Carol said, toeing at the corpse. “He’s actually dead. Actually really dead!” She seemed to be in shock and Bones could understand it – he’d had twelve years where Alexander Marcus didn’t exist, and after that he’d had almost twenty of nominal freedom, but Carol had never been out from under his shadow a day in her life. She stared at Bones with wide eyes, blue and blank, her lips moving silently.

“He’s really, really dead,” Bones said, and it was as though saying the words freed something in him because his next sound was a laugh every bit as wild as Nyota’s, and then he and Carol were flinging themselves at Khan as well, wrapping the augment (who still held his reddened hands out as though he thought maybe they belonged to someone else) in a group hug, all of them kissing any skin they could reach and laughing even though some of them (Bones) had tears on their faces.

Later, there would be explanations. Uhura would explain how she’d hacked John’s collar using upgrades Carol had transferred to her on the Enterprise. They’d release Jim and Spock and explain everything.

Eventually there would be a trial, for John and for Marcus – because if Bones knew his girls, they wouldn’t rest until they’d ground Marcus’ reputation in the mud.

Eventually, there would be a lot of things.

For now they stood, and hugged each other, and breathed free air for the first time in years.

**Notes for the Chapter:**

> Only the epilogue to go now!
> 
> What do you think of my resolution? Too deus ex? 
> 
> Lol Deus Ex Nyota.
> 
> Oh god, I'm nervous because this chapter didn't come out anything like what I was expecting, so please tell me what you thought?


	13. Epilogue

**Notes for the Chapter:**

> And it's done.  
> I can't believe it - can you believe it?

_One year later._

Jim came to see them off. He was supposed to have been three sectors away with the Enterprise, but there are some things that are just more important than orders, and this was one of them.

So walked with Spock out onto the landing pad in the blazing sun, and into the shadow of the ship that sat there.

The _New Beginnings_ was beautiful, even built on a shoestring budget as she was (the settlements had been massive, but spaceships were _very expensive_.) all gleaming pale smoothness and curves like a beautiful woman. She was launching in an hour and people were crawling over her, ant-sized against her bulk, but one of them saw Jim and Spock approaching and called a warning, and a skinny shape came barrelling out of the open cargo doors and intercepted them with a grin as broad as any he’d worn on the _Enterprise_.

“You came!” Doctor McCoy, formerly of Section 31, formerly of Starfleet, now of the _New Beginnings_ , said. “I thought you were supposed to be off looking at a nebula.”

Spock shrugged.

“We thought it would be appropriate to wish you well on your journey,” he said. “The Captain tells me that it is considered appropriate to give a gift on such an occasion.” He held out a wrapped parcel which, Jim knew, contained the entire collected knowledge of Vulcan and Earth uploaded into a datacore he’d built using design specs from the other Spock. “This is for you.”

Bones took it and shook Spock’s hand.

“Thanks, Spock. I appreciate the thought. You want to come and have a look at her before we go?”

Of course they did, and they followed gamely behind Bones as he led the way to the ship. A small group had already assembled at the loading ramp, and Jim exchanged a smile with Uhura and cautious nods with Khan.

“You’re sure you have to go?” he asked.

Khan took Bones’ hand in his and smiled.

“We’re sure,” McCoy said. “There’s still too much prejudice against enhanced humans in the Federation. We could fight for acceptance but in the end…”

“We’re tired, Jim,” Uhura said. “I’m tired of hiding exactly how good I am with computers, and I’m too tired to fight for acceptance here. You people can sort out your own problems, but we won’t be here to see it happen.”

Jim shrugged.

“It was worth a try,” he said. “I suppose we’d better get going before…”

“It will be time to launch soon,” Khan said. “It’s time to be away from here.”

Jim took a step back, then changed his mind and caught McCoy up in a hug, ignoring the looks he got from the crew – Khan’s crew, recovered and revived – as they passed into the belly of the ship.

“Where will you go?” he asked, and Bones laughed.

“Third star to the right, Jim, and straight on till morning.”

Jim let go and stepped back again, his eyes wet.

“Let me know when you get there, okay?” he asked, and his voice may have been a little choked but nobody was going to mention it. Certainly not McCoy, whose eyes glittered suspiciously, or Spock, who was studiously pretending not to see him.

“I will,” Bones said, although of course he would do no such thing and they both knew it.

Jim turned on his heel and strode off, Spock in his wake, to the distant building where they could watch the launch.

Thirty minutes later the spaceship _New Beginnings_ lifted up from the tarmac, and James T. Kirk watched her, and kept watching until she vanished, nothing more than a dwindling light in the fading day.

**Notes for the Chapter:**

> Well, what did you think?  
> I wanted to give everyone a happy ending, and I realised that Khan was never going to have peace as long as he stayed in the Federation, and once it came out that Bones and Nyota were enhanced, neither would they.
> 
> Bonus points to everyone who recognizes the name of their ship, which I stole unrepentantly off Heinlein.
> 
> Sorry that Bones and Khan didn't get together onscreen, but you may take it as read that they do, in fact, get together
> 
> I have a one-shot in this verse planned, just a short PWP that shows their first time, but I don't know when I'll get to it.


End file.
